Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
A+PPA_ r0 c0 MassAction
P+AP_A r1 c0 MassAction
P_A+APAA r2 c0 MassAction
PA_+APAA r3 c0 MassAction

r0 Universal ID's

r0 Text Annotations

r1 Universal ID's

r1 Text Annotations

r2 Universal ID's

r2 Text Annotations

r3 Universal ID's

r3 Text Annotations

Expressions for r0

reaction rate

J

(((Kf * A) * P) - (Kr * PA_)) [uM.s-1]

forward rate constant

Kf

100.0 [s-1.uM-1]

reverse rate constant

Kr

14500.0 [s-1]

Expressions for r1

reaction rate

J

(((Kf * P) * A) - (Kr * P_A)) [uM.s-1]

forward rate constant

Kf

100.0 [s-1.uM-1]

reverse rate constant

Kr

42400.0 [s-1]

Expressions for r2

reaction rate

J

(((Kf * P_A) * A) - (Kr * PAA)) [uM.s-1]

forward rate constant

Kf

100.0 [s-1.uM-1]

reverse rate constant

Kr

14500.0 [s-1]

Expressions for r3

reaction rate

J

(((Kf * PA_) * A) - (Kr * PAA)) [uM.s-1]

forward rate constant

Kf

0.0 [s-1.uM-1]

reverse rate constant

Kr

42400.0 [s-1]

Structures

Name
Type
Electrical
c0 Compartment (+)   (-)

c0 Universal ID's

c0 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
P_A c0 c0
A c0 c0
PAA c0 c0
P c0 c0
PA_ c0 c0

P_A Universal ID's

P_A Text Annotations

A Universal ID's

A Text Annotations

PAA Universal ID's

PAA Text Annotations

P Universal ID's

P Text Annotations

PA_ Universal ID's

PA_ Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application0 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Application0 Universal ID's

Application0 Text Annotations

Specifications (Species) - Application0 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
P_A 0.0 [uM] 0.0 [um2/s] c0
A 41.0 [uM] 0.0 [um2/s] c0
PAA 0.0 [uM] 0.0 [um2/s] c0
P 171.5 [uM] 0.0 [um2/s] c0
PA_ 0.0 [uM] 0.0 [um2/s] c0

Specifications (Reaction) - Application0 go to Simulations

Name
Enabled?
r0 included
r1 included
r2 included
r3 included

Simulations - Application0 go to Specifications

Name
End Time
Output Options
Pin1-FLw/p131_first titration point 1.0

KeepEvery 1

KeepAtMost 1000

Application0 Universal ID's

Application0 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial662221205

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment c0

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Application0.bngl
SBML Application0.sbml
Matlab Application0.m
NFSim XML Application0.xml